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GenomicsSequencing-based ssDNA detection
Meiotic DNA double stranded breaks (DSBs) initiate genetic recombination in discrete areas of the genome called recombination hotspots. Although DSBs can be directly mapped using ChIP-Seq and antibody against ssDNA-associated proteins, genome-wide mapping of recombination hotspots in mammals is stil...
ORGANISM(S): Mus musculus 
2012-02-21 | E-GEOD-34592 | biostudies-arrayexpress
ProteomicsRPA promotes processive ssDNA digestion by Dna2 via their bimodal interaction in Saccharomyces cerevisiae
Single-stranded DNA (ssDNA) widely exists as intermediates in DNA metabolic pathways. The ssDNA binding protein, RPA, not only protects the integrity of ssDNA, but also directs the downstream factor that signals or repairs the ssDNA intermediate. However, it remains unclear how these enzymes/factors...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2022-02-22 | PXD028637 | Pride
Ssdna Saccharomyces cerevisiae Dna2 Rpa 
ProteomicsFor origin melting Rep nucleoprotein complex accommodates both dsDNA and ssDNA of DUE
The replication initiation proteins interact dsDNA located at replication origin and ssDNA of DNA unwinding element (DUE), formed as a result of the destabilization of the double-stranded helix of AT-rich origin region. It is a critical step in the DNA replication initiation; however, the structure ...
ORGANISM(S): Escherichia coli 
2024-01-26 | PXD032398 | Pride
Dna replication Rep proteins Protein-dna interaction Replication initiators Origin opening 
ProteomicsPhase separation properties of RPA combine high-affinity ssDNA binding with dynamic condensate functions at telomeres
RPA has been shown to protect single-stranded DNA (ssDNA) intermediates from instability and breakage. RPA binds ssDNA with sub-nanomolar affinity, yet dynamic turnover is required for downstream ssDNA transactions. How ultrahigh-affinity binding and dynamic turnover are achieved simultaneously is n...
ORGANISM(S): Homo sapiens (Human) 
2023-03-15 | PXD036935 | Pride
Alternative lengthening of telomeres (alt) Replication protein a (rpa) Nuclear organization Biomolecular condensates Genome stability Single-stranded dna (ssdna) 
TranscriptomicsssDNA mapping in dmc1 strains
ssDNA enrichment was used to map and compare DSB hotspots in dmc1, pch2 dmc1, sir2 dmc1, orc1-161 dmc1, dmc1 rdnadelete and dmc1 chr2:12 translocation strains. 6 samples, 2 replicates each. Averaged data is available as a supplementary file on the Series record (below).
ORGANISM(S): Saccharomyces cerevisiae 
2011-08-14 | E-GEOD-30071 | biostudies-arrayexpress
GenomicsStrand-specific ChIP-seq at DNA breaks distinguishes single versus doubled stranded DNA binding and refutes single stranded nucleosomes
Strand-specific ChIP-seq at DNA breaks distinguishes single versus doubled stranded DNA binding and refutes single stranded nucleosomes
PRJNA630205 | ENA
TranscriptomicsssDNA in S phase compared to G1 phase at different timepoints
To identify origins of replication in Lachancea waltii by mapping regions of ssDNA that are enriched in S phase. L. waltii cells are grown in the presence of hydroxyurea, which slows replication forks and causes the accumulation of ssDNA at the replication fork.
ORGANISM(S): Lachancea waltii 
2012-05-09 | E-GEOD-35253 | biostudies-arrayexpress
ProteomicsTEX264 coordinates p97- and SPRTN-mediated resolution of topoisomerase 1-DNA adducts
Eukaryotic topoisomerase 1 (TOP1) regulates DNA topology to ensure efficient DNA replication and transcription. TOP1 is also a major driver of endogenous genome instability, particularly when its catalytic intermediate - a covalent TOP1-DNA adduct known as a TOP1 cleavage complex (TOP1cc) - is stabi...
ORGANISM(S): Homo sapiens (Human) 
2020-03-13 | PXD017239 | Pride
Protein-dna adducts Vcp/p97 Top1 Tex264 Dna repair Genome stability Sprtn Dna replication 
GenomicsQuantitative sensing and signalling of single-stranded DNA during the DNA damage response
Quantitative sensing and signalling of single-stranded DNA during the DNA damage response
PRJNA514440 | ENA
TranscriptomicsMapping of meiotic double-strand break (DSB) sites and DSB factor association near repetitive DNA elements in S. cerevisiae
DNA double strand breaks (DSBs) in repetitive sequences are a potent source of genomic instability, due to the possibility of non-allelic homologous recombination (NAHR). Repetitive sequences are especially at risk during meiosis, when numerous programmed DSBs are introduced into the genome to initi...
ORGANISM(S): Saccharomyces cerevisiae 
2011-08-14 | E-GEOD-30073 | biostudies-arrayexpress
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